current r-forge version fails R CMD check ... ?

stopifnot(identical(ranef(om2), ranef(om3)),

cat('Time elapsed: ', proc.time(),'\n') # for ``statistical reasons''

sessionInfo()

Ben's problem shows up with my implementation, too. Info below.

Reinhold

stopifnot(identical(ranef(m0), ranef(m1)),

+ ? ? ? ? ?identical(ranef(m2), ranef(m3)),
+ ? ? ? ? ?inherits(tryCatch(lmer(y ~ x2|ff + x1, data = D), error =
function(e)e),"error"))
CHOLMOD error: xG? L?R
Fehler: identical(ranef(m0), ranef(m1)) is not TRUE
Zus?tzlich: Warnmeldung:
In Ops.factor(ff, x1) : + nicht sinnvoll f?r Faktoren
+

## Check the use of offset
om2 <- lmer(y ~ x1 + (x2|ff), data = D, offset = x3)
om3 <- lmer(y ~ x1 + (x2|ff) + offset(x3), data = D)

stopifnot(identical(ranef(om2), ranef(om3)),

+ ? ? ? ? ?identical(deviance(om2), deviance(om3)))

if (identical(TRUE, all.equal(fixef(m2), fixef(om2))))

+ ? ?stop("offset does not change the fixed effects")

cat('Time elapsed: ', proc.time(),'\n') # for ``statistical reasons''

Time elapsed: ?11.608 0.369 12.353 0 0

sessionInfo()

R version 2.9.1 (2009-06-26)
i386-apple-darwin8.11.1

locale:
de_DE.UTF-8/en_US.UTF-8/C/C/de_DE.UTF-8/de_DE.UTF-8

attached base packages:
[1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods
[7] base

other attached packages:
[1] lme4_0.999375-31 ? Matrix_0.999375-29 lattice_0.17-25

loaded via a namespace (and not attached):
[1] grid_2.9.1

On Sat, Aug 1, 2009 at 6:31 PM, Ben Bolker<bolker at ufl.edu> wrote:

?I don't mind it being public.

?I got similar results with the CRAN lme4 (0.999375-31),
with Matrix ...-30. ?BATCH fails on m2 != m3 (consistently);
source() fails on m0 != m1.

?I'm probably doing something really really dumb, would appreciate
anyone else who can try this on their systems ...

?If you don't feel like downloading or running all of lmer-1.R, the
following code chunk should demonstrate the problem ...

=================
library(lme4)

set.seed(1)
## Wrong formula gave a seg.fault at times:
D <- ?data.frame(y= rnorm(20,10), ff = gl(4,5),
? ? ? ? ? ? ? ? x1=rnorm(20,3), x2=rnorm(20,7),
? ? ? ? ? ? ? ? x3=rnorm(20,1))
m0 <- lmer(y ~ (x1 + x2)|ff, data = D)
m1 <- lmer(y ~ x1 + x2|ff ?, data = D)
m2 <- lmer(y ~ x1 + (x2|ff), data = D)
m3 <- lmer(y ~ (x2|ff) + x1, data = D)
stopifnot(identical(ranef(m0), ranef(m1)),
? ? ? ? ?identical(ranef(m2), ranef(m3)),
? ? ? ? ?inherits(tryCatch(lmer(y ~ x2|ff + x1, data = D), error =
function(e)e),
? ? ? ? ? ? ? ? ? "error"))

## Check the use of offset
om2 <- lmer(y ~ x1 + (x2|ff), data = D, offset = x3)
om3 <- lmer(y ~ x1 + (x2|ff) + offset(x3), data = D)

stopifnot(identical(ranef(om2), ranef(om3)),
? ? ? ? ?identical(deviance(om2), deviance(om3)))
if (identical(TRUE, all.equal(fixef(m2), fixef(om2))))
? ?stop("offset does not change the fixed effects")

cat('Time elapsed: ', proc.time(),'\n') # for ``statistical reasons''


Martin Maechler wrote:

Hi Ben,
as you took this "private", I'd like at least Doug Bates
to be in the CC ..
Personally I would prefer to have this continue in the R-SIG-ME list
rather than privately... ?I'll be pretty offline from now till Monday
in any case

On Fri, Jul 31, 2009 at 20:17, Ben Bolker<bolker at ufl.edu> wrote:

Martin Maechler wrote:

"BB" == Ben Bolker <bolker at ufl.edu>
? ? on Thu, 30 Jul 2009 17:30:17 -0400 writes:

? ? BB> When I use the latest r-forge version of lme4
? ? BB> ( ?0.999375-32 ) it seems to fail R CMD check on a tiny
? ? BB> numerical mismatch of two objects that are supposed
? ? BB> (??) to be identical (I also
? ? BB> get a mangled CHOLMOD error message, but I suspect that
? ? BB> comes from somewhere within Matrix ...)

yes, and those should be gone with the version of Matrix
(0.999375-30) of two days ago.

? ? BB> can anyone confirm?

No. ?To the contrary.
I have had a slightly updated version of tests/lmer-1.Rout.save
ready to be committed for a while, but that's only trivial
changes.

and below, from your sessionInfo(), it looks like you are using
a current version of R and packages ...
hmm ...

Regards,
Martin


? ? BB> can anyone confirm? any ideas for a fix?


? ? BB> The offending mismatch between ranef(m2) and ranef(m3)
? ? BB> is very small ...

well; it's interesting that the offending mismatch in the error
message below is between ?m0 and m1, ?...

?hmmm indeed. ?Maybe I was already hacking things. ?I have
(1) updated Matrix, (2) installed lme4 directly from r-forge.
sessionInfo() says

?lme4_0.999375-32 ? Matrix_0.999375-30

in ../tests, I do

R --vanilla
library(lme4)
source("lmer-1.R",echo=TRUE)

or

R CMD BATCH --vanilla lmer-1.R

?oddly, the second (BATCH) always fails on m0/m1; the
first (source) fails at different comparisons (sometimes m0/m1;
sometimes m2/m3; sometimes om2/om3 in the next section ... ???

I just can't understand how that *can* happen.
It would mean that the algorithms used were slightly "random", ?or
e.g. using slightly different precision depending on memory
allocation, or ??,
???

As I said i the first e-mail: The slightly different formula should
produce absolutely identical matrices and vectors which define the
loglikelihood (or RE-LogLik.) and then the minimization really should
be 100% reproducible on a given R+Platform+Installed-Packages setup.

I assume you have tried the same with the CRAN-version of lme4 ...
which has exactly the same tests/lmer-1.R ??
....
the phenomenon looks so illogical, ?I even start to wonder if it's a
bug in your computer (hardware-low-level software combination)?
Maybe you could ask again on R-SIg-ME if others could reproduce?

BTW: Have you noticed that we (Doug Bates and I, when at the
useR/DSC meetings) have moved the former 'allcoef' branch into a
``regular R-forge package'' ?called ?'lme4a'

?yes.

But yes, that definitely does not pass 'CMD check at the moment'.

? ? >> getwd()
? ? BB> [1] "/home/ben/lib/R/pkgs/lme4/pkg/lme4/tests"

? ? >> source("lmer-1.R",echo=TRUE)

? ? BB> ...
? ? >> D <- ?data.frame(y= rnorm(20,10), ff = gl(4,5),
? ? BB> x1=rnorm(20,3), x2=rnorm(20,7),
? ? BB> x3=rnorm(20,1))
? ? >> m0 <- lmer(y ~ (x1 + x2)|ff, data = D)
? ? >> m1 <- lmer(y ~ x1 + x2|ff ?, data = D)

We had added these checks exactly *because* we wanted to be sure
that a slightly different use of formulas would lead to the
identical 'X', 'Z', .... matrices, and L(theta)
parametrizations,
so I wonder how your version of lme4 could give different
results here....

? ? >> m2 <- lmer(y ~ x1 + (x2|ff), data = D)
? ? >> m3 <- lmer(y ~ (x2|ff) + x1, data = D)
? ? >> stopifnot(identical(ranef(m0), ranef(m1)),
? ? BB> + ? ? ? ? ? identical(ranef(m2), ranef(m3)),
? ? BB> + ? ? ? ? ? inherits(tryCatch(lmer(y ~ x2|ff + x1, data = D) ....
? ? BB> [TRUNCATED]
? ? BB> CHOLMOD error: =*?1????@???T??o????
? ? BB> Error: identical(ranef(m0), ranef(m1)) is not TRUE
? ? BB> In addition: Warning message:
? ? BB> In Ops.factor(ff, x1) : + not meaningful for factors

Note that the cholmod error and warning is from the
? ?lmer(y ~ x2|ff + x1, data = D)
part {which is wrapped in ?tryCatch(...)}.

Also, if I execute

##----------------------------------------------------
D <- ?data.frame(y= rnorm(20,10), ff = gl(4,5),
? ? ? ? ? ? ? ? ?x1=rnorm(20,3), x2=rnorm(20,7),
? ? ? ? ? ? ? ? ?x3=rnorm(20,1))
m0 <- lmer(y ~ (x1 + x2)|ff, data = D)
m1 <- lmer(y ~ x1 + x2|ff ?, data = D)
m2 <- lmer(y ~ x1 + (x2|ff), data = D)
m3 <- lmer(y ~ (x2|ff) + x1, data = D)
stopifnot(identical(ranef(m0), ranef(m1)),
? ? ? ? ? identical(ranef(m2), ranef(m3)))
cat("Ok\n")
##----------------------------------------------------

many times, I never see a problem.

Are you sure you are not using your already-hacked version of
lme4 ???

Martin Maechler, ETH Zurich

?I'm not 100.0000% sure, but I don't see how I could be ...

?Ben

--
Ben Bolker
Associate professor, Biology Dep't, Univ. of Florida
bolker at ufl.edu / www.zoology.ufl.edu/bolker
GPG key: www.zoology.ufl.edu/bolker/benbolker-publickey.asc